macOS Installation Instructions
Table of Contents
Apple Command Line Tools
Apple provides a suite of “command line tools” to facilitate computer
programming, and these tools include git which we will use
for this workshop. To install the command line tools, open the
Terminal application by searching for “Terminal” in
Spotlight:
A note on using Terminal: Terminal will likely (and often atwhen you first start using it!) prompt you messages like, “Terminal would like to access files on Desktop.” If/when you see this message, always agree! Agreeing allows your Terminal to access your computer’s file system.
When Terminal is open, type xcode-select --install into
the Terminal and press Enter, which will reveal a message as
follows:
Shortly after, a separate window will pop up prompting you to install
command line tools, where you should click Install:
A license agreement will then appear, which you should
Agree to in order to continue with the installation:
Finally, command line tools will install, and you can follow its progress in this window that will appear. Importantly, this screen tends to first appear with outrageous installation times, like 165 hours (!) below. Don’t panic! These outrageous times will drop quickly, and the whole process will really take about 10-20 minutes.
R and RStudio
This workshop does not require a specific R or RStudio version for this workshop. If you already have R and RStudio installed, you can skip this section!
Installing R
First, navigate to the CRAN website in the browser: https://cran.r-project.org/. Click the link
Download R for macOS:
On the next page, click the link to install the Intel
64-bit of R, R-4.2.0.pkg (blue box in the image
below). This Intel version will still work on M1 computers. We do
NOT recommend installing the Apple silicon arm64
(crossed out in the image below) build because it tends to conflict with
some Bioconductor packages which you may want to use in your own
research.
Open the downloaded R installer, and follow instructions to install R
onto your computer. Make sure to agree to the license in the setup menu
and give your computer’s password when prompted!
Installing the RStudio IDE
First, navigate to the RStudio Download page website in the browser: https://www.rstudio.com/products/rstudio/download/. Click the link to Download the Free version of RStudio Desktop.
Next, click the large link to Download RStudio for Mac:
Open the downloaded RStudio installer, and follow instructions to
install it onto your computer. Note that if you’re using an Apple
Silicon (M1) chip, you may be prompted to install something called
Rosetta 2 in order to use RStudio. Rosetta 2
is a software made by Apple to support the Intel to M1 transition, and
it is currently needed to run RStudio on M1 chips. If prompted to
install Rosetta 2, agree to the prompt and follow
instructions accordingly.
Installing necessary R packages
For this workshop, you will need to have the following R packages
installed: + tidyverse + rmarkdown +
optparse + renv
If you already have these packages installed, you’re good to go!
Otherwise, open RStudio (this assumes both R and RStudio have been
installed). You can check if these packages are installed by scrolling
through the Packages tab in the bottom-right pane of
RStudio. If you see the package of interest listed, then you know it’s
installed. For example, the image below tells us that
optparse is already installed and no additional action is
required to install this package:
If you need to install any of the require packages, use the function
install.packages() in Console, as follows:
# Install optparse only:
install.packages("optparse")
# Install rmarkdown only:
install.packages("rmarkdown")
# Install tidyverse only:
install.packages("tidyverse")
# Install renv only:
install.packages("renv")
# Or, you can install several simultaneously
# For example, this installs optparse and renv :
install.packages(c("optparse", "renv"))After running this/these command(s), you will see some progress
messages pass in Console (maybe in a different color from this image,
but that’s ok!!). The following image shows, for example, what these
messages look like for a successful installation of
optparse:
Note: While installing packages, you may be prompted to install Command Line Tools if you didn’t install it already. If you see this message, agree to it and follow all installation steps for Command Line Tools.
GitKraken
We will use the GUI (graphical user interface) called
GitKraken to work with git in this workshop.
This GUI can be installed from https://www.gitkraken.com/, where you can click
“Download GitKraken Client Free” (do not pay!!):
Then, select the appropriate version for your computer’s architecture.
The GitKraken installer will now download, and when completed, open it and follow all installation instructions.
A suitable text editor
macOS comes with a “text editor” program called “TextEdit.” In spite of its compelling name, this is NOT a recommend text editor for writing computer code! Please do not use TextEdit!
Instead, we recommend you obtain one of the following (free versions!) of these more robust text editors: